Thousands of foreign criminals who have been convicted of offences outside England and Wales have had their DNA profiles and fingerprint details deleted from British police databases, a Home Office watchdog has revealed.

Alastair MacGregor QC, the biometrics commissioner, has warned the Home Office that this “obviously unsatisfactory state of affairs” might be putting the public at unnecessary risk.

The commissioner says there is a gap in the law as a result of new rules designed to remove DNA profiles and fingerprints of innocent people from the police national computer.

He says this gap means the biometric details of those arrested but not charged with an offence in Britain cannot be held indefinitely solely because they have been convicted of an offence outside England and Wales.

“If the police wish to retain the biometric records of such individuals and have no other basis for doing so, they have no option but to go back to those individuals and (re-arresting them) to take further samples and fingerprints from them,” said the commissioner, voicing concern about the burden this places on forces.

MacGregor says re-arresting and re-sampling a suspect following his conviction outside England and Wales could prove a greater invasion of their privacy than simply holding onto the DNA and fingerprints samples already taken from them.

The commissioner also says rules that restrict the holding of DNA and fingerprint details of foreign-national criminals on the police national computer of foreign criminals have severely limited the practical use of the powers for British police forces.

“The police have been and remain unable to take and retain … biometric material from many EU nationals who they know have been convicted of qualifying offences under England and Wales,” said the watchdog.

In his first annual report the commissioner cites the case of an EU national who had been arrested but not charged with burglary whose details could not be kept despite the fact that he had served more than 13 years in prison in another European country for similar offences. MacGregor says he made an exception for that case but his DNA profile and fingerprints could only be retained for a much shorter period than would otherwise have been the case.

A Home Office spokesperson said: “This government has ended the heavy-handed system under which the DNA of innocent people was kept indefinitely – but we will never put the public at risk.

“We have ensured the police have retained the power to take and keep DNA and fingerprints from any EU national living in the UK when they represent a threat to the public and have been convicted abroad of a crime which is the equivalent of a serious offence in England and Wales ...

“The UK requests and uses more data about foreign offenders than almost any other country. We are one of the biggest users of the European criminal records system and are leading the way in Europe to encourage the proactive sharing of information about individuals who could pose a risk to the public.”

The biometrics commissioner also raises technical problems with ensuring the DNA and fingerprints of individuals convicted of offences in Scotland and Northern Ireland are on the police national computer for England and Wales. He says that ministers are considering the possibility of seeking legislation to cater for some of these problems.

A separate report from the national DNA database strategy board says that the removal of 1.7m DNA profiles taken from innocent people and children as a result of Theresa May’s Protection of Freedoms Act 2012 has not led to any reduction in the number of matches the database procduces.

“In the quarter from 1 April to 30 June 2014, the database produced 37 matches to murder, 127 to rapes and 6,111 to other crime scenes. In the same quarter of 2013, when the old system for retaining DNA was in effect, it produced 37 matches to murder, 103 to rapes and 6,141 to other crime scenes,” it reports.